Method of characterizing a tumor based on an immune gene expression signature in regulatory T cell (Treg)-enriched tumor samples

Abstract

An immune gene expression signature is associated with favorable clinical features in Treg-enriched tumor samples and can be used to predict immunogenicity of a tumor, overall survival, and/or chemosensitivity.

What is claimed is: 
     
       1. A method of characterizing a tumor, comprising:
 quantifying or obtaining expression strength for a plurality of differentially expressed genes, wherein the genes are differentially expressed in an immune competent cell in the tumor, wherein the plurality of differentially expressed genes comprise at least six of PCDHA5, EFNA5, BARX2, DPP4, CEMP1, SSX1, CD70, LTB, LILRA4, TRAV9.2, GZMM, ZAP70, CD3E, SIRPG, CD3D, SIT1, CD27, CTLA4, ICOS, CD5, GPR171, SH2D1A, TRAT1, ITK, CD3G, RYR1, LAIR2, NTN3, PMCH, GPR1, PLCH2, and BCL11B, and wherein the immune competent cell is a regulatory T cell (Treg); 
 associating the expression strengths with a cluster representative of overall patient survival, immunogenicity of the tumor, and/or chemosensitivity of the tumor; and 
 using the association to thereby characterize the tumor as being associated with prolonged overall patient survival, immunogenicity of the tumor, and/or chemosensitivity of the tumor. 
 
     
     
       2. The method of  claim 1 , further comprising a step of calculating an immunophenoscore. 
     
     
       3. The method of  claim 1 , wherein the plurality of differentially expressed genes comprise PCDHA5, EFNA5, BARX2, DPP4, CEMP1, SSX1, CD70, LTB, LILRA4, TRAV9.2, GZMM, ZAP70, CD3E, SIRPG, CD3D, SIT1, CD27, CTLA4, ICOS, CD5, GPR171, SH2D1A, TRAT1, ITK, CD3G, RYR1, LAIR2, NTN3, PMCH, GPR1, PLCH2, and BCL11B. 
     
     
       4. The method of  claim 1 , wherein the step of quantifying or obtaining expression strength uses previously obtained transcriptomics data. 
     
     
       5. The method of  claim 1 , wherein the step of quantifying or obtaining expression strength uses a tumor sample. 
     
     
       6. The method of  claim 1 , wherein the expression strength is determined from RNAseq data. 
     
     
       7. The method of  claim 1 , wherein the tumor is enriched in Treg cells. 
     
     
       8. The method of  claim 1 , wherein the tumor is enriched in CD8+ T cells. 
     
     
       9. The method of  claim 1 , wherein the tumor is enriched in M1 macrophages cells. 
     
     
       10. The method of  claim 1 , wherein the tumor has elevated expression of a check point marker. 
     
     
       11. The method of  claim 1 , further comprising a step of determining immune cell composition in the tumor. 
     
     
       12. The method of  claim 1 , further comprising a step of performing a DNA accessibility prediction on the tumor. 
     
     
       13. The method of  claim 1 , wherein the plurality of differentially expressed genes are highly differentially expressed genes in Treg cells. 
     
     
       14. The method of  claim 1  wherein the cancer is bladder cancer (BLCA), lung adenocarcinoma (LUAD), pancreatic adenocarcinoma (PAAD), skin cutaneous melanoma (SKCM), and stomach adenocarcinoma (STAD). 
     
     
       15. The method of  claim 1 , further comprising a step of administering chemotherapy upon characterization of the tumor as being chemosensitive. 
     
     
       16. The method of  claim 1 , further comprising a step of administering immune therapy upon characterization of the tumor as being immunogenic.